Quite a complex situation you have here, cats are intellectual beings despite being domesticated they still have the longing for the wild. I guessed your cat must have experience something during her stay outside that made her feel more at ease than being at home. I have never had a cat but from my general knowledge of pet, staying inside for too long makes them feel suffocated. I believe if you can let her out in a garden or probably take her out on a walk once in awhile might help a little.